Endpoint detection of amplified nucleic acids

Meagher, Robert; Koh, Chung-Yan; Light, Yooli Kim; Ball, Cameron Scott

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Title: Endpoint detection of amplified nucleic acids

Abstract

The present invention relates to probes and primers beneficial for conducting amplification assays, such as those including loop-mediated isothermal amplification reactions. Also described herein are methods for detecting targets using such probes and/or primers.

Inventors:: Meagher, Robert; Koh, Chung-Yan; Light, Yooli Kim; Ball, Cameron Scott

Issue Date:: 2022-10-18

Research Org.:: Sandia National Lab. (SNL-CA), Livermore, CA (United States)

Sponsoring Org.:: USDOE; National Institute of Allergy and Infectious Diseases (NIAID)

OSTI Identifier:: 1986709

Patent Number(s):: 11473141

Application Number:: 16/903,075

Assignee:: National Technology & Engineering Solutions of Sandia, LLC (Albuquerque, NM)

DOE Contract Number:: AC04-94AL85000; R01AI098853

Resource Type:: Patent

Resource Relation:: Patent File Date: 06/16/2020

Country of Publication:: United States

Language:: English

Citation Formats


                    Meagher, Robert, Koh, Chung-Yan, Light, Yooli Kim, and Ball, Cameron Scott. Endpoint detection of amplified nucleic acids.  United States: N. p., 2022. 
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                    Meagher, Robert, Koh, Chung-Yan, Light, Yooli Kim, & Ball, Cameron Scott. Endpoint detection of amplified nucleic acids.  United States.

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                    Meagher, Robert, Koh, Chung-Yan, Light, Yooli Kim, and Ball, Cameron Scott. Tue .  
        "Endpoint detection of amplified nucleic acids".  United States.  https://www.osti.gov/servlets/purl/1986709.

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@article{osti_1986709,

  title        = {Endpoint detection of amplified nucleic acids},

  author       = {Meagher, Robert and Koh, Chung-Yan and Light, Yooli Kim and Ball, Cameron Scott},

  abstractNote = {The present invention relates to probes and primers beneficial for conducting amplification assays, such as those including loop-mediated isothermal amplification reactions. Also described herein are methods for detecting targets using such probes and/or primers.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2022},

  month        = {10}

}

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Title: Endpoint detection of amplified nucleic acids

Abstract

Citation Formats

Development of a multiplex loop-mediated isothermal amplification (mLAMP) method for the simultaneous detection of bovine Babesia parasites journal, December 2007

System and method for detecting components of a mixture including a valving scheme for competition assays patent, July 2017

Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue journal, March 2009

Epidemiology and Transmission Dynamics of West Nile Virus Disease journal, August 2005

Simultaneous detection and quantitation of Chikungunya, Dengue and West Nile viruses by multiplex RT-PCR assays and Dengue virus typing using High Resolution Melting journal, December 2009

Detection of Loop-Mediated Isothermal Amplification Reaction by Turbidity Derived from Magnesium Pyrophosphate Formation journal, November 2001

Method for Detecting Target Nucleic Acid patent-application, November 2014

Stability of Loop-Mediated Isothermal Amplification (LAMP) Reagents and its Amplification Efficiency on Crude Trypanosome DNA Templates journal, January 2009

Identification of common molecular subsequences journal, March 1981

Multiplex Amplification and Detection patent-application, June 2012

Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation patent, February 2015

Sequence-specific detection method for reverse transcription, loop-mediated isothermal amplification of HIV-1 journal, June 2009

Loop-Mediated Isothermal Amplification for Direct Detection of Mycobacterium tuberculosis Complex, M. avium, and M. intracellulare in Sputum Samples journal, June 2003

Detection of amplification products patent, July 2015

PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation journal, June 1997

Pharmaceutical Salts journal, January 1977

Homogenous, real-time duplex loop-mediated isothermal amplification using a single fluorophore-labeled primer and an intercalator dye: Its application to the simultaneous detection of Shiga toxin genes 1 and 2 in Shiga toxigenic Escherichia coli isolates journal, August 2010

Rapid and Real-Time Detection of Chikungunya Virus by Reverse Transcription Loop-Mediated Isothermal Amplification Assay journal, November 2006

Methods and reagents for amplifying nucleic acids patent, November 2017

Detection of amplification products patent, July 2015

Chikungunya: A Potentially Emerging Epidemic? journal, April 2010

Loop-Mediated Isothermal Amplification (LAMP) Method for Rapid Detection of Trypanosoma brucei rhodesiense journal, February 2008

Methods for detecting bacteriophage MS2 patent, September 2007

Compositions and Methods for the Detection of a Nucleic Acid Using a Cleavage Reaction patent-application, February 2008

Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification for Rapid Detection of West Nile Virus journal, January 2004

Quantitative detection of pathogens in centrifugal microfluidic disks patent, February 2018

Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification journal, June 2006

Toxin activity assays, devices, methods and systems therefor patent, April 2016

Detection of Amplification Products patent-application, January 2014

Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation patent, April 2016

Rapid detection of HIV-1 by reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) journal, August 2008

Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes journal, February 2015

Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products journal, April 2008

Hand-Held Wireless Platform and Optics for Measurement of DNA, RNA, MicroRNAs, and Other Markers of Pathogens, Genetic Diseases, and Cancer patent-application, July 2014

Basic local alignment search tool journal, October 1990

Comparison of biosequences journal, December 1981

Isothermal Amplification Using a Chemical Heating Device for Point-of-Care Detection of HIV-1 journal, February 2012

Detection of Acute HIV-1 Infection by RT-LAMP journal, May 2015

Loop‐Mediated Isothermal Amplification for Detection of Nucleic Acids journal, January 2014

Devices, systems, and methods for detecting nucleic acids using sedimentation patent, October 2017

Loop-mediated isothermal amplification (LAMP): recent progress in research and development journal, January 2013

Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases journal, January 2009

Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid patent, October 2017

Simultaneous multiple target detection in real-time loop-mediated isothermal amplification journal, August 2012

Process for synthesizing nucleic acid patent, June 2002

Method for Amplifying Nucleic Acid and Analysis of Single-Nucleotide Polymorphism Using the Same patent-application, December 2005

Composition and methods for rapid detection of HIV by loop-mediated isothermal amplification (LAMP) patent, December 2014

RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests journal, February 2011

Clinical burden of chikungunya virus infection journal, January 2008

Loop-mediated isothermal amplification of DNA journal, June 2000

Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications journal, June 2011

Micropores and methods of making and using thereof patent, November 2013

Quenching of Unincorporated Amplification Signal Reporters in Reverse-Transcription Loop-Mediated Isothermal Amplification Enabling Bright, Single-Step, Closed-Tube, and Multiplexed Detection of RNA Viruses journal, March 2016

Sequence Specific Real-Time Monitoring Of Loop-Mediated Isothermal amplification (LAMP) patent-application, July 2013

Novel Micropores and Methods of Making and Using Thereof patent-application, April 2014

Accelerated reaction by loop-mediated isothermal amplification using loop primers journal, June 2002

Diagnostic assay for cancer patent, February 2001

Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus journal, September 2015

Mechanistic Evaluation of the Pros and Cons of Digital RT-LAMP for HIV-1 Viral Load Quantification on a Microfluidic Device and Improved Efficiency via a Two-Step Digital Protocol journal, January 2013

Detection of metabolites for controlled substances patent, April 2019

Development of a multiplex loop-mediated isothermal amplification (mLAMP) method for the simultaneous detection of bovine Babesia parasites
journal, December 2007

System and method for detecting components of a mixture including a valving scheme for competition assays
patent, July 2017

Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue
journal, March 2009

Epidemiology and Transmission Dynamics of West Nile Virus Disease
journal, August 2005

Simultaneous detection and quantitation of Chikungunya, Dengue and West Nile viruses by multiplex RT-PCR assays and Dengue virus typing using High Resolution Melting
journal, December 2009

Detection of Loop-Mediated Isothermal Amplification Reaction by Turbidity Derived from Magnesium Pyrophosphate Formation
journal, November 2001

Method for Detecting Target Nucleic Acid
patent-application, November 2014

Stability of Loop-Mediated Isothermal Amplification (LAMP) Reagents and its Amplification Efficiency on Crude Trypanosome DNA Templates
journal, January 2009

Identification of common molecular subsequences
journal, March 1981

Multiplex Amplification and Detection
patent-application, June 2012

Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation
patent, February 2015

Sequence-specific detection method for reverse transcription, loop-mediated isothermal amplification of HIV-1
journal, June 2009

Loop-Mediated Isothermal Amplification for Direct Detection of Mycobacterium tuberculosis Complex, M. avium, and M. intracellulare in Sputum Samples
journal, June 2003

Detection of amplification products
patent, July 2015

PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation
journal, June 1997

Pharmaceutical Salts
journal, January 1977

Homogenous, real-time duplex loop-mediated isothermal amplification using a single fluorophore-labeled primer and an intercalator dye: Its application to the simultaneous detection of Shiga toxin genes 1 and 2 in Shiga toxigenic Escherichia coli isolates
journal, August 2010

Rapid and Real-Time Detection of Chikungunya Virus by Reverse Transcription Loop-Mediated Isothermal Amplification Assay
journal, November 2006

Methods and reagents for amplifying nucleic acids
patent, November 2017

Detection of amplification products
patent, July 2015

Chikungunya: A Potentially Emerging Epidemic?
journal, April 2010

Loop-Mediated Isothermal Amplification (LAMP) Method for Rapid Detection of Trypanosoma brucei rhodesiense
journal, February 2008

Methods for detecting bacteriophage MS2
patent, September 2007

Compositions and Methods for the Detection of a Nucleic Acid Using a Cleavage Reaction
patent-application, February 2008

Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification for Rapid Detection of West Nile Virus
journal, January 2004

Quantitative detection of pathogens in centrifugal microfluidic disks
patent, February 2018

Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification
journal, June 2006

Toxin activity assays, devices, methods and systems therefor
patent, April 2016

Detection of Amplification Products
patent-application, January 2014

Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation
patent, April 2016

Rapid detection of HIV-1 by reverse-transcription, loop-mediated isothermal amplification (RT-LAMP)
journal, August 2008

Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes
journal, February 2015

Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products
journal, April 2008

Hand-Held Wireless Platform and Optics for Measurement of DNA, RNA, MicroRNAs, and Other Markers of Pathogens, Genetic Diseases, and Cancer
patent-application, July 2014

Basic local alignment search tool
journal, October 1990

Comparison of biosequences
journal, December 1981

Isothermal Amplification Using a Chemical Heating Device for Point-of-Care Detection of HIV-1
journal, February 2012

Detection of Acute HIV-1 Infection by RT-LAMP
journal, May 2015

Loop‐Mediated Isothermal Amplification for Detection of Nucleic Acids
journal, January 2014

Devices, systems, and methods for detecting nucleic acids using sedimentation
patent, October 2017

Loop-mediated isothermal amplification (LAMP): recent progress in research and development
journal, January 2013

Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases
journal, January 2009

Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid
patent, October 2017

Simultaneous multiple target detection in real-time loop-mediated isothermal amplification
journal, August 2012

Process for synthesizing nucleic acid
patent, June 2002

Method for Amplifying Nucleic Acid and Analysis of Single-Nucleotide Polymorphism Using the Same
patent-application, December 2005

Composition and methods for rapid detection of HIV by loop-mediated isothermal amplification (LAMP)
patent, December 2014

RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests
journal, February 2011

Clinical burden of chikungunya virus infection
journal, January 2008

Loop-mediated isothermal amplification of DNA
journal, June 2000

Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications
journal, June 2011

Micropores and methods of making and using thereof
patent, November 2013

Quenching of Unincorporated Amplification Signal Reporters in Reverse-Transcription Loop-Mediated Isothermal Amplification Enabling Bright, Single-Step, Closed-Tube, and Multiplexed Detection of RNA Viruses
journal, March 2016

Sequence Specific Real-Time Monitoring Of Loop-Mediated Isothermal amplification (LAMP)
patent-application, July 2013

Novel Micropores and Methods of Making and Using Thereof
patent-application, April 2014

Accelerated reaction by loop-mediated isothermal amplification using loop primers
journal, June 2002

Diagnostic assay for cancer
patent, February 2001

Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus
journal, September 2015

Mechanistic Evaluation of the Pros and Cons of Digital RT-LAMP for HIV-1 Viral Load Quantification on a Microfluidic Device and Improved Efficiency via a Two-Step Digital Protocol
journal, January 2013

Detection of metabolites for controlled substances
patent, April 2019